Re: Calculate energy of a residue using NAMD energy

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Wed Jan 31 2018 - 17:25:13 CST

Hi Peter,

I am using VMD installed on the cluster so I have no idea whether they have
installed the latest version. I used the syntax given in the link you sent
but, that's the error I get. May be I should first try the script with VMD
on my personal computer so that I can track the error.

Thanks anyway.
Best,
Monika

On Wed, Jan 31, 2018 at 12:51 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> Dear Monika,
> namdenergy is a proper vmd plugin. Is there any reason that you're trying
> to use an old downloaded version rather than using the package that comes
> with vmd?
> package require namdenergy
> should make the text interface available. See http://www.ks.uiuc.edu/
> Research/vmd/plugins/namdenergy/ for how to use it.
> Best,
> Peter
>
> On Mon, Jan 29, 2018 at 10:22 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
> wrote:
>
>> Dear all,
>>
>> I want to calculate the total energy of a specific residue (a water
>> molecule) at each frame. It is suggested that this can be done using NAMD
>> energy plugin. However, I would like to do the job through a script because
>> my trajectory is in a remote server.
>>
>> I tried the following.
>> obtained the code in this link and created a .tcl file called
>> namdenergy.tcl in the folder where I have my script.
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-
>> 7277/namdenergy.tcl
>>
>> Then I wrote a different tcl script with
>> source namdenergy.tcl
>> namd energy -all -sel $sel -par myparameterfile.inp
>>
>> Here I specified the parameter file because my parameter file is
>> different from the common charmm parameter file. However, I am getting the
>> following error
>>
>> invalid command name "::FinderTool::find"
>>
>> I would be grateful for a guidence to correctly use the namd energy to
>> calculate energies of some selected atomselections.
>>
>> Thank you.
>> Best,
>> Monika
>>
>> --
>> W.A.Monika Madhavi
>> Lecturer (Probation),
>> Department of Physics,
>> University of Colombo.
>>
>
>

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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